CHECK report for LineagePulse on malbec1
This page was generated on 2019-04-16 11:53:12 -0400 (Tue, 16 Apr 2019).
LineagePulse 1.2.1
David S Fischer
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/LineagePulse |
| Branch: RELEASE_3_8 |
| Last Commit: 1ec2a20 |
| Last Changed Date: 2019-01-04 13:15:17 -0400 (Fri, 04 Jan 2019) |
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ WARNINGS ] | |  |
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
Summary
Command output
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### Running command:
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### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:LineagePulse.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings LineagePulse_1.2.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/LineagePulse.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘LineagePulse/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘LineagePulse’ version ‘1.2.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘LineagePulse’ can be installed ... WARNING
Found the following significant warnings:
Note: possible error in 'evalLogLikGeneMM(vecCounts = vecCounts, ': unused arguments (matDispParam = matDispParam, matDropParam = matDropParam, matWeights = matWeights)
Note: possible error in 'evalLogLikGeneMM(vecCounts = vecCounts, ': unused arguments (matDispParam = do.call(cbind, lapply(seq_len(ncol(matWeights)), function(m) vecDispParam)), matDropParam = do.call(cbind, lapply(seq_len(ncol(matWeights)), function(m) vecPiParam)), matWeights = matWeights)
See ‘/home/biocbuild/bbs-3.8-bioc/meat/LineagePulse.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
decompressDispByGeneMM: no visible binding for global variable
‘lsDispModel’
evalLogLikMatrix : <anonymous>: possible error in
evalLogLikGeneMM(vecCounts = vecCounts, matMuParam = matMuParam,
vecNormConst = lsMuModel$lsMuModelGlobal$vecNormConst, matDispParam =
matDispParam, matDropParam = matDropParam, matWeights = matWeights,
vecidxNotZero = which(!is.na(vecCounts) & vecCounts > 0), vecidxZero
= which(!is.na(vecCounts) & vecCounts == 0), scaNCells =
length(vecCounts)): unused arguments (matDispParam = matDispParam,
matDropParam = matDropParam, matWeights = matWeights)
evalLogLikMatrix : <anonymous>: possible error in
evalLogLikGeneMM(vecCounts = vecCounts, matMuParam = do.call(cbind,
lapply(seq_len(ncol(matWeights)), function(m) vecMuParam)),
vecNormConst = lsMuModel$lsMuModelGlobal$vecNormConst, matDispParam =
do.call(cbind, lapply(seq_len(ncol(matWeights)), function(m)
vecDispParam)), matDropParam = do.call(cbind,
lapply(seq_len(ncol(matWeights)), function(m) vecPiParam)),
matWeights = matWeights, vecidxNotZero = which(!is.na(vecCounts) &
vecCounts > 0), vecidxZero = which(!is.na(vecCounts) & vecCounts ==
0), : unused arguments (matDispParam = do.call(cbind,
lapply(seq_len(ncol(matWeights)), function(m) vecDispParam)),
matDropParam = do.call(cbind, lapply(seq_len(ncol(matWeights)),
function(m) vecPiParam)), matWeights = matWeights)
evalLogLikMatrix : <anonymous>: possible error in scaNCells =
length(vecCounts)): unused arguments (matDispParam = do.call(cbind,
lapply(seq_len(ncol(matWeights)), function(m) vecDispParam)),
matDropParam = do.call(cbind, lapply(seq_len(ncol(matWeights)),
function(m) vecPiParam)), matWeights = matWeights)
plotCellDensity: no visible binding for global variable ‘continuous’
plotGene: no visible binding for global variable ‘x’
plotGene: no visible binding for global variable ‘dropout_posterior’
plotGene: no visible binding for global variable ‘groups’
plotGene: no visible binding for global variable ‘dfAnnot’
plotGene: no visible binding for global variable ‘mean_count’
plotGene: no visible binding for global variable ‘quantile_25’
plotGene: no visible binding for global variable ‘quantile_75’
plotGene: no visible binding for global variable ‘model’
plotGene: no visible binding for global variable ‘continuous’
plotGene: no visible binding for global variable ‘trajectory_contour’
plotGene: no visible binding for global variable ‘ncells’
Undefined global functions or variables:
continuous dfAnnot dropout_posterior groups lsDispModel mean_count
model ncells quantile_25 quantile_75 trajectory_contour x
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotCellDensity 42.396 0.092 42.548
accessors 17.124 0.284 17.543
getFitsMean 16.420 0.024 16.491
cash-LineagePulseObject-method 16.312 0.024 16.365
names-LineagePulseObject-method 15.896 0.008 15.938
getNormData 15.712 0.036 15.807
sub-sub-LineagePulseObject-character-missing-method 15.728 0.016 15.763
getFitsDispersion 15.096 0.024 15.134
getFitsDropout 15.032 0.040 15.085
getPostDrop 14.832 0.024 14.886
writeReport 14.716 0.008 14.751
runLineagePulse 12.680 0.016 12.711
plotGene 12.232 0.004 12.249
sortGeneTrajectories 12.148 0.028 12.193
testDropout 10.892 0.012 10.912
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 1 NOTE
See
‘/home/biocbuild/bbs-3.8-bioc/meat/LineagePulse.Rcheck/00check.log’
for details.
Installation output
LineagePulse.Rcheck/00install.out
Tests output
Example timings
LineagePulse.Rcheck/LineagePulse-Ex.timings